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- PDB-2k62: NMR solution structure of the supramolecular adduct between a liv... -

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Basic information

Entry
Database: PDB / ID: 2k62
TitleNMR solution structure of the supramolecular adduct between a liver cytosolic bile acid binding protein and a bile acid-based Gd(III)-chelate
ComponentsLiver fatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / hepatospecific contrast agent / HADDOCK / Gd(III) bile acid adduct / Acetylation / Cytoplasm / Lipid-binding / Transport
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-ITL / YTTERBIUM (III) ION / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
Model detailsThis is the first solution structure of the complex between a bile acid binding protein and a ...This is the first solution structure of the complex between a bile acid binding protein and a synthetic chelate of a bile acid adduct with Gd(III), a model for a new hepatospecific contrast agent.
AuthorsTomaselli, S. / Zanzoni, S. / Ragona, L. / Gianolio, E. / Aime, S. / Assfalg, M. / Molinari, H.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Solution structure of the supramolecular adduct between a liver cytosolic bile acid binding protein and a bile acid-based gadolinium(III)-chelate, a potential hepatospecific magnetic resonance ...Title: Solution structure of the supramolecular adduct between a liver cytosolic bile acid binding protein and a bile acid-based gadolinium(III)-chelate, a potential hepatospecific magnetic resonance imaging contrast agent.
Authors: Tomaselli, S. / Zanzoni, S. / Ragona, L. / Gianolio, E. / Aime, S. / Assfalg, M. / Molinari, H.
History
DepositionJul 3, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Liver fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0963
Polymers14,1001
Non-polymers9962
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Liver fatty acid-binding protein / L-FABP / Liver basic FABP / LB- FABP / Liver bile acid-binding protein / L-BABP


Mass: 14100.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FABP1 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / References: UniProt: P80226
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-ITL / (3alpha,5alpha,8alpha)-3-[(N,N-bis{2-[bis(carboxymethyl)amino]ethyl}-L-gamma-glutamyl)amino]cholan-24-oic acid


Mass: 822.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H66N4O13

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is the first solution structure of the complex between a bile acid binding protein and a synthetic chelate of a bile acid adduct with Gd(III), a model for a new hepatospecific contrast agent.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.3 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.03 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Haddock water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 7

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